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- PDB-5wyq: Crystal Structure and catalytic mechanism of the essential m1G37 ... -

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Basic information

Entry
Database: PDB / ID: 5wyq
TitleCrystal Structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / Pseudomonas aeruginosa PA14 / tRNA (m1G37) methyltransferase / TrmD / tDNA modification
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA N1-guanine methylation / cytosol
Similarity search - Function
tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase TrmD / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases ...tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase TrmD / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsJaroensuk, J. / Liew, C.W. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Zhong, W. / McBee, M.E. / Maenpuen, S. / Prestwich, E.G. / DeMott, M.S. ...Jaroensuk, J. / Liew, C.W. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Zhong, W. / McBee, M.E. / Maenpuen, S. / Prestwich, E.G. / DeMott, M.S. / Mongkolsuk, S. / Dedon, P.C. / Lescar, J. / Fuangthong, M. / Chaiyen, P.
CitationJournal: Rna / Year: 2019
Title: Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD fromPseudomonas aeruginosa.
Authors: Jaroensuk, J. / Wong, Y.H. / Zhong, W. / Liew, C.W. / Maenpuen, S. / Sahili, A.E. / Atichartpongkul, S. / Chionh, Y.H. / Nah, Q. / Thongdee, N. / McBee, M.E. / Prestwich, E.G. / DeMott, M.S. ...Authors: Jaroensuk, J. / Wong, Y.H. / Zhong, W. / Liew, C.W. / Maenpuen, S. / Sahili, A.E. / Atichartpongkul, S. / Chionh, Y.H. / Nah, Q. / Thongdee, N. / McBee, M.E. / Prestwich, E.G. / DeMott, M.S. / Chaiyen, P. / Mongkolsuk, S. / Dedon, P. / Lescar, J. / Fuangthong, M.
History
DepositionJan 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (guanine-N(1)-)-methyltransferase
B: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5264
Polymers55,7292
Non-polymers7972
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-19 kcal/mol
Surface area21120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.896, 85.896, 147.838
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 27864.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: trmD, PA14_15990 / Plasmid: pNIC-CH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q02RL6, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris-Cl pH 8.4, 12% MPD, 12% PEG 1000, 12% PEG 3350, 5% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 18, 2015 / Details: Toroidal focusing
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→28.12 Å / Num. obs: 34505 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 51.63 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.9
Reflection shellResolution: 2.16→2.29 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2943 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P9P

1p9p


Resolution: 2.16→28.12 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.214 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.184
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1741 5.05 %RANDOM
Rwork0.207 ---
obs0.209 34499 99.9 %-
Displacement parametersBiso mean: 59.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.169 Å20 Å20 Å2
2--0.169 Å20 Å2
3----0.338 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.16→28.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 54 180 4038
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013945HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.025340HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1410SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes672HARMONIC5
X-RAY DIFFRACTIONt_it3945HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion18.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion491SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4564SEMIHARMONIC4
LS refinement shellResolution: 2.16→2.23 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2804 131 4.45 %
Rwork0.261 2810 -
all0.2618 2941 -
obs--99.7 %

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